ConsensusMapDF#

class pyopenms.dataframes.ConsensusMapDF(*args, **kwargs)#

Bases: pyopenms.pyopenms_1.ConsensusMap

__init__(*args, **kwargs)#

Cython signature: void ConsensusMap()
Cython signature: void ConsensusMap(ConsensusMap &)

Methods

`__init__`(args, *kwargs)	Cython signature: void ConsensusMap()
`appendColumns`	Cython signature: ConsensusMap appendColumns(ConsensusMap) Add consensus map entries as new columns
`appendRows`	Cython signature: ConsensusMap appendRows(ConsensusMap) Add consensus map entries as new rows
`clear`	Cython signature: void clear(bool clear_meta_data)
`clearMetaInfo`	Cython signature: void clearMetaInfo() Removes all meta values
`clearRanges`	Cython signature: void clearRanges() Resets all range dimensions as empty
`clearUniqueId`	Cython signature: size_t clearUniqueId() Clear the unique id.
`empty`	Cython signature: bool empty()
`ensureUniqueId`	Cython signature: size_t ensureUniqueId() Assigns a valid unique id, but only if the present one is invalid.
`getColumnHeaders`
`getDataProcessing`	Cython signature: libcpp_vector[DataProcessing] getDataProcessing() Returns a const reference to the description of the applied data processing
`getExperimentType`	Cython signature: String getExperimentType() Non-mutable access to the experiment type
`getIdentifier`	Cython signature: String getIdentifier() Retrieve document identifier (e.g.
`getKeys`	Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set
`getLoadedFilePath`	Cython signature: String getLoadedFilePath() Returns the file_name which is the absolute path to the file loaded
`getLoadedFileType`	Cython signature: int getLoadedFileType() Returns the file_type (e.g.
`getMaxIntensity`	Cython signature: double getMaxIntensity() Returns the maximum intensity
`getMaxMZ`	Cython signature: double getMaxMZ() Returns the maximum m/z
`getMaxRT`	Cython signature: double getMaxRT() Returns the maximum RT
`getMetaValue`	Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or
`getMinIntensity`	Cython signature: double getMinIntensity() Returns the minimum intensity
`getMinMZ`	Cython signature: double getMinMZ() Returns the minimum m/z
`getMinRT`	Cython signature: double getMinRT() Returns the minimum RT
`getPrimaryMSRunPath`	Cython signature: void getPrimaryMSRunPath(StringList & toFill) Returns the MS run path (stored in ColumnHeaders)
`getProteinIdentifications`	Cython signature: libcpp_vector[ProteinIdentification] getProteinIdentifications()
`getUnassignedPeptideIdentifications`	Cython signature: libcpp_vector[PeptideIdentification] getUnassignedPeptideIdentifications()
`getUniqueId`	Cython signature: size_t getUniqueId() Returns the unique id
`get_df`()	Generates a pandas DataFrame with both consensus feature meta data and intensities from each sample.
`get_intensity_df`()	Generates a pandas DataFrame with feature intensities from each sample in long format (over files).
`get_metadata_df`()	Generates a pandas DataFrame with feature meta data (sequence, charge, mz, RT, quality).
`hasInvalidUniqueId`	Cython signature: size_t hasInvalidUniqueId() Returns whether the unique id is invalid.
`hasValidUniqueId`	Cython signature: size_t hasValidUniqueId() Returns whether the unique id is valid.
`isMetaEmpty`	Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty
`isValid`	Cython signature: bool isValid(uint64_t unique_id) Returns true if the unique_id is valid, false otherwise
`metaRegistry`	Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry
`metaValueExists`	Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists
`push_back`	Cython signature: void push_back(ConsensusFeature spec)
`removeMetaValue`	Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists
`reserve`	Cython signature: void reserve(size_t s)
`setColumnHeaders`
`setDataProcessing`	Cython signature: void setDataProcessing(libcpp_vector[DataProcessing]) Sets the description of the applied data processing
`setExperimentType`	Cython signature: void setExperimentType(String experiment_type) Mutable access to the experiment type
`setIdentifier`	Cython signature: void setIdentifier(String id) Sets document identifier (e.g.
`setLoadedFilePath`	Cython signature: void setLoadedFilePath(String file_name) Sets the file_name according to absolute path of the file loaded, preferably done whilst loading
`setLoadedFileType`	Cython signature: void setLoadedFileType(String file_name) Sets the file_type according to the type of the file loaded from, preferably done whilst loading
`setMetaValue`	Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name
`setPrimaryMSRunPath`	Cython signature: void setPrimaryMSRunPath(StringList & s)
`setProteinIdentifications`	Cython signature: void setProteinIdentifications(libcpp_vector[ProteinIdentification]) Sets the protein identifications
`setUnassignedPeptideIdentifications`	Cython signature: void setUnassignedPeptideIdentifications(libcpp_vector[PeptideIdentification]) Sets the unassigned peptide identifications
`setUniqueId`	Cython signature: void setUniqueId(uint64_t rhs) Assigns a new, valid unique id.
`setUniqueIds`
`size`	Cython signature: int size()
`sortByIntensity`	Cython signature: void sortByIntensity(bool reverse)
`sortByMZ`	Cython signature: void sortByMZ() Sorts the peaks according to m/z position
`sortByMaps`	Cython signature: void sortByMaps() Sorts with respect to the sets of maps covered by the consensus features (lexicographically)
`sortByPosition`	Cython signature: void sortByPosition() Lexicographically sorts the peaks by their position (First RT then m/z)
`sortByQuality`	Cython signature: void sortByQuality(bool reverse)
`sortByRT`	Cython signature: void sortByRT() Sorts the peaks according to RT position
`sortBySize`	Cython signature: void sortBySize() Sorts with respect to the size (number of elements)
`sortPeptideIdentificationsByMapIndex`	Cython signature: void sortPeptideIdentificationsByMapIndex() Sorts PeptideIdentifications of consensus features with respect to their map index.
`updateRanges`	Cython signature: void updateRanges()

appendColumns()#: Cython signature: ConsensusMap appendColumns(ConsensusMap) Add consensus map entries as new columns

appendRows()#: Cython signature: ConsensusMap appendRows(ConsensusMap) Add consensus map entries as new rows

clear()#

Cython signature: void clear(bool clear_meta_data) Clears all data and meta data
Cython signature: void clear()

clearMetaInfo()#: Cython signature: void clearMetaInfo() Removes all meta values

clearRanges()#: Cython signature: void clearRanges() Resets all range dimensions as empty

clearUniqueId()#: Cython signature: size_t clearUniqueId() Clear the unique id. The new unique id will be invalid. Returns 1 if the unique id was changed, 0 otherwise

empty()#: Cython signature: bool empty()

ensureUniqueId()#: Cython signature: size_t ensureUniqueId() Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was changed, 0 otherwise

getColumnHeaders()#

getDataProcessing()#: Cython signature: libcpp_vector[DataProcessing] getDataProcessing() Returns a const reference to the description of the applied data processing

getExperimentType()#: Cython signature: String getExperimentType() Non-mutable access to the experiment type

getIdentifier()#: Cython signature: String getIdentifier() Retrieve document identifier (e.g. an LSID)

getKeys()#: Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set

getLoadedFilePath()#: Cython signature: String getLoadedFilePath() Returns the file_name which is the absolute path to the file loaded

getLoadedFileType()#: Cython signature: int getLoadedFileType() Returns the file_type (e.g. featureXML, consensusXML, mzData, mzXML, mzML, …) of the file loaded

getMaxIntensity()#: Cython signature: double getMaxIntensity() Returns the maximum intensity

getMaxMZ()#: Cython signature: double getMaxMZ() Returns the maximum m/z

getMaxRT()#: Cython signature: double getMaxRT() Returns the maximum RT

getMetaValue()#: Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or

getMinIntensity()#: Cython signature: double getMinIntensity() Returns the minimum intensity

getMinMZ()#: Cython signature: double getMinMZ() Returns the minimum m/z

getMinRT()#: Cython signature: double getMinRT() Returns the minimum RT

getPrimaryMSRunPath()#: Cython signature: void getPrimaryMSRunPath(StringList & toFill) Returns the MS run path (stored in ColumnHeaders)

getProteinIdentifications()#: Cython signature: libcpp_vector[ProteinIdentification] getProteinIdentifications()

getUnassignedPeptideIdentifications()#: Cython signature: libcpp_vector[PeptideIdentification] getUnassignedPeptideIdentifications()

getUniqueId()#: Cython signature: size_t getUniqueId() Returns the unique id

get_df()#

Generates a pandas DataFrame with both consensus feature meta data and intensities from each sample.

Returns: pandas.DataFrame: meta data and intensity DataFrame

get_intensity_df()#

Generates a pandas DataFrame with feature intensities from each sample in long format (over files).

For labelled analyses channel intensities will be in one row, therefore resulting in a semi-long/block format. Resulting DataFrame can be joined with result from get_metadata_df by their index ‘id’.

Returns: pandas.DataFrame: intensity DataFrame

get_metadata_df()#

Generates a pandas DataFrame with feature meta data (sequence, charge, mz, RT, quality).

Resulting DataFrame can be joined with result from get_intensity_df by their index ‘id’.

Returns: pandas.DataFrame: DataFrame with metadata for each feature (such as: best identified sequence, charge, centroid RT/mz, fitting quality)

hasInvalidUniqueId()#: Cython signature: size_t hasInvalidUniqueId() Returns whether the unique id is invalid. Returns 1 if the unique id is invalid, 0 otherwise

hasValidUniqueId()#: Cython signature: size_t hasValidUniqueId() Returns whether the unique id is valid. Returns 1 if the unique id is valid, 0 otherwise

isMetaEmpty()#: Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty

isValid()#: Cython signature: bool isValid(uint64_t unique_id) Returns true if the unique_id is valid, false otherwise

metaRegistry()#: Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry

metaValueExists()#: Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists

push_back()#: Cython signature: void push_back(ConsensusFeature spec)

removeMetaValue()#: Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists

reserve()#: Cython signature: void reserve(size_t s)

setColumnHeaders()#

setDataProcessing()#: Cython signature: void setDataProcessing(libcpp_vector[DataProcessing]) Sets the description of the applied data processing

setExperimentType()#: Cython signature: void setExperimentType(String experiment_type) Mutable access to the experiment type

setIdentifier()#: Cython signature: void setIdentifier(String id) Sets document identifier (e.g. an LSID)

setLoadedFilePath()#: Cython signature: void setLoadedFilePath(String file_name) Sets the file_name according to absolute path of the file loaded, preferably done whilst loading

setLoadedFileType()#: Cython signature: void setLoadedFileType(String file_name) Sets the file_type according to the type of the file loaded from, preferably done whilst loading

setMetaValue()#: Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name

setPrimaryMSRunPath()#

Cython signature: void setPrimaryMSRunPath(StringList & s) Sets the file paths to the primary MS run (stored in ColumnHeaders)
Cython signature: void setPrimaryMSRunPath(StringList & s, MSExperiment & e)

setProteinIdentifications()#: Cython signature: void setProteinIdentifications(libcpp_vector[ProteinIdentification]) Sets the protein identifications

setUnassignedPeptideIdentifications()#: Cython signature: void setUnassignedPeptideIdentifications(libcpp_vector[PeptideIdentification]) Sets the unassigned peptide identifications

setUniqueId()#: Cython signature: void setUniqueId(uint64_t rhs) Assigns a new, valid unique id. Always returns 1

setUniqueIds()#

size()#: Cython signature: int size()

sortByIntensity()#

Cython signature: void sortByIntensity(bool reverse) Sorts the peaks according to ascending intensity.
Cython signature: void sortByIntensity()

sortByMZ()#: Cython signature: void sortByMZ() Sorts the peaks according to m/z position

sortByMaps()#: Cython signature: void sortByMaps() Sorts with respect to the sets of maps covered by the consensus features (lexicographically)

sortByPosition()#: Cython signature: void sortByPosition() Lexicographically sorts the peaks by their position (First RT then m/z)

sortByQuality()#

Cython signature: void sortByQuality(bool reverse) Sorts the peaks according to ascending quality.
Cython signature: void sortByQuality()

sortByRT()#: Cython signature: void sortByRT() Sorts the peaks according to RT position

sortBySize()#: Cython signature: void sortBySize() Sorts with respect to the size (number of elements)

sortPeptideIdentificationsByMapIndex()#: Cython signature: void sortPeptideIdentificationsByMapIndex() Sorts PeptideIdentifications of consensus features with respect to their map index.

updateRanges()#: Cython signature: void updateRanges()